The Right of a Superior Species: Averted by responsible Superior Species, who understand why it’s not a good idea to go around granting yourself an Omniscient Morality License. (Even if the traditional tactless way to put it is along the lines of “The corollary of being a Superior Species is the responsibility to behave in a manner befitting a [morally] Superior Species.”)
Has the Empire ever faced up with a species/polity that don’t avert the trope?
None that actually qualified; a fairly large number that though they did, would be the short answer.
(The closest possible situations to that scenario, though, go by the name of perversions, and are the subject of serious containment efforts – like, say, the Leviathan Consciousness.)